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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ), 'gf_id' => 'HOM05D001176', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001176' ), 'data_identifier' => 'HOM05D001176', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001176', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '528', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p18860' => 'bna', 'A02p29190' => 'bna', 'A04p04910' => 'bna', 'A07p21400' => 'bna', 'A08p10400' => 'bna', 'A08p11660' => 'bna', 'A09p34560' => 'bna', 'A09p34570' => 'bna', 'A09p46140' => 'bna', 'Aa31LG10G8300' => 'aar', 'Aa31LG2G14290' => 'aar', 'Aa31LG9G2280' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2586' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.2648' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5147' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.799' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2951' => 'aag', 'Actinidia01255' => 'ach', 'Actinidia03827' => 'ach', 'Actinidia12511' => 'ach', 'Actinidia26638' => 'ach', 'Actinidia32787' => 'ach', 'Ah.03g147660' => 'amhyb', 'Ah.05g167880' => 'amhyb', 'Ah.15g091370' => 'amhyb', 'AL1G45850' => 'aly', 'AL1G45870' => 'aly', 'AL5G34010' => 'aly', 'AL7G40600' => 'aly', 'Aqoxy1G01043' => 'aox', 'Aqoxy2G00588' => 'aox', 'Aqoxy2G03809' => 'aox', 'Aqoxy7G00899' => 'aox', 'arahy.Tifrunner.gnm1.ann1.12WBQG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.570P5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7XHH75' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F8T0MB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GLV5L5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M1JRW6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NAXY0P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V0K3WG' => 'arhy', 'AT1G31780' => 'ath', 'AT1G31800' => 'ath', 'AT3G53130' => 'ath', 'AT4G15110' => 'ath', 'ATR0088G045' => 'atr', 'ATR0661G531' => 'atr', 'ATR0665G266' => 'atr', 'ATR0772G108' => 'atr', 'ATR0815G009' => 'atr', 'ATR1094G004' => 'atr', 'ATR1094G011' => 'atr', 'ATR1094G015' => 'atr', 'ATR1094G023' => 'atr', 'Atru.chr12.2158' => 'acertr', 'Atru.chr8.1001' => 'acertr', 'Atru.chr8.1712' => 'acertr', 'Atru.chr8.2633' => 'acertr', 'AUR62000370' => 'cqu', 'AUR62003539' => 'cqu', 'AUR62006725' => 'cqu', 'AUR62014932' => 'cqu', 'AUR62015049' => 'cqu', 'AUR62017508' => 'cqu', 'AUR62017853' => 'cqu', 'AUR62026972' => 'cqu', 'AUR62029077' => 'cqu', 'BcaB01g01054' => 'bca', 'BcaB04g18125' => 'bca', 'BcaB04g18283' => 'bca', 'BcaB07g32825' => 'bca', 'BcaC01g01099' => 'bca', 'BcaC02g12235' => 'bca', 'BcaC02g12620' => 'bca', 'BcaC04g21501' => 'bca', 'BcaC05g27192' => 'bca', 'BcaC07g37726' => 'bca', 'BcaC07g37872' => 'bca', 'BcaC07g37873' => 'bca', 'BcaC07g37875' => 'bca', 'BcaC09g48232' => 'bca', 'BolC1t03958H' => 'bol', 'BolC4t21752H' => 'bol', 'BolC4t22238H' => 'bol', 'BolC5t31821H' => 'bol', 'BolC5t31822H' => 'bol', 'BolC6t37285H' => 'bol', 'BolC8t48109H' => 'bol', 'BolC8t48266H' => 'bol', 'BolC8t48268H' => 'bol', 'BraA01t01829Z' => 'bra', 'BraA04t16204Z' => 'bra', 'BraA07t29827Z' => 'bra', 'BraA08t33039Z' => 'bra', 'BraA08t33160Z' => 'bra', 'BraA09t38996Z' => 'bra', 'BraA09t40077Z' => 'bra', 'C03p88080' => 'bna', 'C05p30980' => 'bna', 'C05p30990' => 'bna', 'C05p62050' => 'bna', 'C06p21010' => 'bna', 'CAN.G1272.1' => 'can', 'CAN.G1598.1' => 'can', 'CAN.G276.8' => 'can', 'CAN.G4.31' => 'can', 'CAN.G541.26' => 'can', 'CAN.G598.8' => 'can', 'CAN.G930.8' => 'can', 'CANSAT11G0194' => 'cansat', 'CANSAT64G1576' => 'cansat', 'CANSAT78G1928' => 'cansat', 'CARHR031080' => 'chi', 'CARHR031100' => 'chi', 'CARHR162980' => 'chi', 'CARHR221850' => 'chi', 'Carub.0001s3008' => 'cru', 'Carub.0001s3010' => 'cru', 'Carub.0005s1966' => 'cru', 'Carub.0007s2688' => 'cru', 'Ca_07959_v3' => 'car', 'Ca_11534_v3' => 'car', 'Ca_11536_v3' => 'car', 'Ca_11539_v3' => 'car', 'Ca_24495_v3' => 'car', 'Ca_25034_v3' => 'car', 'CBR_g21846' => 'cbr', 'CBR_g41079' => 'cbr', 'CBR_g4469' => 'cbr', 'CBR_g55238' => 'cbr', 'CBR_g61501' => 'cbr', 'CBR_g61503' => 'cbr', 'Cc05_g00020' => 'ccan', 'Cc06_g04720' => 'ccan', 'Cc07_g20650' => 'ccan', 'Cc08_g05630' => 'ccan', 'Cc09_g03290' => 'ccan', 'CDE02G2271' => 'cde', 'CDE02G4052' => 'cde', 'CDE04G2738' => 'cde', 'CDE06G1242' => 'cde', 'CDE08G0683' => 'cde', 'CDE08G1160' => 'cde', 'CDE08G1691' => 'cde', 'Cfa006301' => 'cfa', 'Cfa016465' => 'cfa', 'Cfa022496' => 'cfa', 'Cfa027119' => 'cfa', 'Cfa027341' => 'cfa', 'Ciclev10011152m.g' => 'ccl', 'Ciclev10011312m.g' => 'ccl', 'Ciclev10011353m.g' => 'ccl', 'Ciclev10011420m.g' => 'ccl', 'CiPaw.04G072600' => 'cil', 'CiPaw.07G075100' => 'cil', 'CiPaw.09G004700' => 'cil', 'CiPaw.11G075700' => 'cil', 'ClCG04G009570' => 'cla', 'ClCG07G010970' => 'cla', 'ClCG10G008080' => 'cla', 'ClCG11G016030' => 'cla', 'COL.COLO4_00003' => 'col', 'COL.COLO4_11286' => 'col', 'COL.COLO4_22248' => 'col', 'COL.COLO4_27432' => 'col', 'COL.COLO4_33764' => 'col', 'Cpa.g.sc123.11' => 'cpa', 'Cpa.g.sc123.12' => 'cpa', 'Cpa.g.sc5.131' => 'cpa', 'Cpa.g.sc8.285' => 'cpa', 'Cpa.g.sc90.31' => 'cpa', 'Cre01.g027550' => 'cre', 'Cre02.g142266' => 'cre', 'Cre02.g144250' => 'cre', 'Cre08.g373100' => 'cre', 'Cre13.g587750' => 'cre', 'Cre16.g659200' => 'cre', 'Cre16.g678437' => 'cre', 'CsaV3_3G007050' => 'csa', 'CsaV3_4G007300' => 'csa', 'CsaV3_4G027950' => 'csa', 'CsaV3_4G027980' => 'csa', 'CsaV3_6G040180' => 'csa', 'CSS0004945' => 'camsi', 'CSS0012136' => 'camsi', 'CSS0022319' => 'camsi', 'CSS0027781' => 'camsi', 'CSS0028297' => 'camsi', 'CSS0030107' => 'camsi', 'CSS0037928' => 'camsi', 'DCAR_001483' => 'dca', 'DCAR_013342' => 'dca', 'DCAR_017658' => 'dca', 'DCAR_023843' => 'dca', 'Dinv05894' => 'din', 'Dinv37353' => 'din', 'Dinv41808' => 'din', 'Dinv41809' => 'din', 'Dinv44680' => 'din', 'Duzib106G0318' => 'dzi', 'Duzib106G0985' => 'dzi', 'Duzib128G0007' => 'dzi', 'Duzib138G1658' => 'dzi', 'Duzib205G1840' => 'dzi', 'ECA234G0291' => 'eca', 'ECA238G2945' => 'eca', 'ECA238G4204' => 'eca', 'ECA240G2428' => 'eca', 'ECA248G1435' => 'eca', 'ECA248G2999' => 'eca', 'EL10Ac4g09433' => 'bvu', 'EL10Ac5g11241' => 'bvu', 'EL10Ac6g15342' => 'bvu', 'EL10Ac7g16711' => 'bvu', 'Eucgr.A00911' => 'egr', 'Eucgr.A01599' => 'egr', 'Eucgr.D02557' => 'egr', 'Eucgr.H01373' => 'egr', 'FAN02G1694' => 'fan', 'FAN02G3300' => 'fan', 'FAN05G1696' => 'fan', 'FAN05G2373' => 'fan', 'FAN05G2872' => 'fan', 'FAN05G5118' => 'fan', 'FAN09G2605' => 'fan', 'FAN09G3806' => 'fan', 'FAN14G2976' => 'fan', 'FAN14G4358' => 'fan', 'FAN14G4971' => 'fan', 'FAN15G1703' => 'fan', 'FAN15G2248' => 'fan', 'FAN20G0920' => 'fan', 'FAN27G0701' => 'fan', 'FvH4_2g37280' => 'fve', 'FvH4_6g00890' => 'fve', 'FvH4_6g17140' => 'fve', 'FvH4_6g39510' => 'fve', 'Glyma.01G154450' => 'gma', 'Glyma.01G154501' => 'gma', 'Glyma.01G154551' => 'gma', 'Glyma.01G226502' => 'gma', 'Glyma.09G252800' => 'gma', 'Glyma.10G062900' => 'gma', 'Glyma.11G016200' => 'gma', 'Glyma.11G090100' => 'gma', 'Glyma.13G147500' => 'gma', 'Glyma.18G239900' => 'gma', 'Gohir.A07G184400' => 'ghi', 'Gohir.A08G149700' => 'ghi', 'Gohir.A11G323100' => 'ghi', 'Gohir.A13G154700' => 'ghi', 'Gohir.D07G191200' => 'ghi', 'Gohir.D08G170700' => 'ghi', 'Gohir.D08G170800' => 'ghi', 'Gohir.D11G342200' => 'ghi', 'Gohir.D13G159400' => 'ghi', 'Gorai.001G213800' => 'gra', 'Gorai.004G178200' => 'gra', 'Gorai.007G372200' => 'gra', 'Gorai.013G180200' => 'gra', 'GSVIVG01013198001' => 'vvi', 'GSVIVG01015850001' => 'vvi', 'GSVIVG01019158001' => 'vvi', 'GSVIVG01033707001' => 'vvi', 'HanXRQChr01g0025791' => 'han', 'HanXRQChr01g0028241' => 'han', 'HanXRQChr03g0068151' => 'han', 'HanXRQChr17g0559051' => 'han', 'Haze_02517' => 'cav', 'Haze_04494' => 'cav', 'Haze_04497' => 'cav', 'Haze_13645' => 'cav', 'Haze_19470' => 'cav', 'Hma1.2p1_2774F.1_g328270' => 'hma', 'HPP92_003369' => 'vpl', 'HPP92_004191' => 'vpl', 'HPP92_015168' => 'vpl', 'HPP92_018761' => 'vpl', 'HPP92_018762' => 'vpl', 'Hund16023' => 'sun', 'Hund20285' => 'sun', 'Hund21873' => 'sun', 'Lalb_Chr03g0038311' => 'lal', 'Lalb_Chr05g0211481' => 'lal', 'Lalb_Chr09g0324961' => 'lal', 'Lalb_Chr16g0380331' => 'lal', 'Lalb_Chr21g0315241' => 'lal', 'Lj1A1044G23' => 'lonja', 'Lj1g0018224' => 'lja', 'Lj2C52G4' => 'lonja', 'Lj2g0027044' => 'lja', 'Lj3A994T59' => 'lonja', 'Lj5g0025528' => 'lja', 'Lj9C202G6' => 'lonja', 'LjContig00222g0002891' => 'lja', 'Lsat_1_v5_gn_1_52661' => 'lsa', 'Lsat_1_v5_gn_1_58321' => 'lsa', 'Lsat_1_v5_gn_2_16321' => 'lsa', 'Lsat_1_v5_gn_6_23680' => 'lsa', 'Lsat_1_v5_gn_9_124460' => 'lsa', 'Manes.08G016300' => 'mes', 'Manes.09G079657' => 'mes', 'Manes.09G183600' => 'mes', 'Manes.15G189800' => 'mes', 'Mapoly0009s0222' => 'mpo', 'Mapoly0011s0135' => 'mpo', 'Mapoly0028s0136' => 'mpo', 'Mapoly0245s0001' => 'mpo', 'MBI04_g37458_MAGBIO' => 'mbi', 'MBI10_g09189_MAGBIO' => 'mbi', 'MBI18_g15121_MAGBIO' => 'mbi', 'MBI18_g19460_MAGBIO' => 'mbi', 'MBI18_g31363_MAGBIO' => 'mbi', 'MBI18_g38520_MAGBIO' => 'mbi', 'MBI18_g44466_MAGBIO' => 'mbi', 'MCO03G158' => 'mco', 'MCO06G124' => 'mco', 'MCO06G252' => 'mco', 'MCO07G473' => 'mco', 'MCO10G170' => 'mco', 'MCO16G584' => 'mco', 'MD04G1239800' => 'mdo', 'MD12G1257000' => 'mdo', 'MD13G1243800' => 'mdo', 'MD13G1243900' => 'mdo', 'MD13G1244000' => 'mdo', 'MD14G1097800' => 'mdo', 'MD17G1129200' => 'mdo', 'Medtr1g062190' => 'mtr', 'Medtr5g009110' => 'mtr', 'Medtr5g025410' => 'mtr', 'Medtr7g079440' => 'mtr', 'MELO3C010519.2' => 'cme', 'MELO3C014945.2' => 'cme', 'MELO3C016233.2' => 'cme', 'MELO3C024495.2' => 'cme', 'Migut.A00530' => 'egut', 'Migut.F02071' => 'egut', 'Migut.J00470' => 'egut', 'Migut.M00093' => 'egut', 'MSTRG.19204' => 'ama', 'MSTRG.25741' => 'ama', 'MSTRG.6599' => 'ama', 'MSTRG.9229' => 'ama', 'Nitab4.5_0000019g0160' => 'nta', 'Nitab4.5_0000030g0410' => 'nta', 'Nitab4.5_0000132g0440' => 'nta', 'Nitab4.5_0000456g0030' => 'nta', 'Nitab4.5_0001333g0050' => 'nta', 'Nitab4.5_0003650g0010' => 'nta', 'Nitab4.5_0005208g0020' => 'nta', 'Nitab4.5_0009814g0010' => 'nta', 'Nitab4.5_0018702g0010' => 'nta', 'Nn1g03127' => 'nnu', 'Nn1g08468' => 'nnu', 'Nn1g09379' => 'nnu', 'Nn2g13887' => 'nnu', 'Nn3g19881' => 'nnu', 'Nn6g35182' => 'nnu', 'Nn7g38267' => 'nnu', 'Nn7g38268' => 'nnu', 'Oeu010179.1' => 'oeu', 'Oeu010181.1' => 'oeu', 'Oeu012378.4' => 'oeu', 'Oeu014108.2' => 'oeu', 'Oeu039635.2' => 'oeu', 'Oeu041470.1' => 'oeu', 'Oeu054597.1' => 'oeu', 'Os02g0173100' => 'osa', 'Os02g0817900' => 'osa', 'Os03g0225600' => 'osa', 'Os10g0546600' => 'osa', 'Peaxi162Scf00110g00819' => 'pax', 'Peaxi162Scf00193g00811' => 'pax', 'Peaxi162Scf00215g00510' => 'pax', 'Peaxi162Scf00322g00310' => 'pax', 'PGR004G1849' => 'pgr', 'PGR031G0231' => 'pgr', 'PGR031G1111' => 'pgr', 'PGR031G2625' => 'pgr', 'PGSC0003DMG400001956' => 'stu', 'PGSC0003DMG400024342' => 'stu', 'PGSC0003DMG400028180' => 'stu', 'Phvul.002G121100' => 'pvu', 'Phvul.002G165400' => 'pvu', 'Phvul.007G226500' => 'pvu', 'Phvul.008G056400' => 'pvu', 'Potri.004G236600' => 'ptr', 'Potri.006G006200' => 'ptr', 'Potri.006G119800' => 'ptr', 'Potri.013G088100' => 'ptr', 'Pp3c2_23210' => 'ppa', 'Pp3c4_28160' => 'ppa', 'Pp3c5_28020' => 'ppa', 'Pp3c6_15960' => 'ppa', 'PRCOL_00001498' => 'pco', 'PRCOL_00001869' => 'pco', 'PRCOL_00002320' => 'pco', 'PRCOL_00004323' => 'pco', 'PRCOL_00005745' => 'pco', 'PRCOL_00007072' => 'pco', 'Prupe.1G077200' => 'ppe', 'Prupe.3G185900' => 'ppe', 'Prupe.6G358000' => 'ppe', 'Prupe.7G123500' => 'ppe', 'Psat0s1223g0080' => 'psa', 'Psat2g146720' => 'psa', 'Psat2g186080' => 'psa', 'Psat3g105040' => 'psa', 'Psat6g077400' => 'psa', 'PSO017G2236' => 'pso', 'PSO063G1081' => 'pso', 'PSO339G0330' => 'pso', 'PSO541G0961' => 'pso', 'PSO675G4847' => 'pso', 'PSO675G7478' => 'pso', 'PSO732G0580' => 'pso', 'QL01p050622' => 'qlo', 'QL04p062166' => 'qlo', 'QL07p041486' => 'qlo', 'QL11p012635' => 'qlo', 'QL12p003889' => 'qlo', 'RcHm_v2.0_Chr2g0153541' => 'rch', 'RcHm_v2.0_Chr3g0448381' => 'rch', 'RcHm_v2.0_Chr3g0471231' => 'rch', 'RcHm_v2.0_Chr6g0304421' => 'rch', 'Rhsim01G0115800' => 'rsi', 'Rhsim01G0201000' => 'rsi', 'Rhsim04G0139400' => 'rsi', 'Rhsim04G0139800' => 'rsi', 'Rhsim05G0168700' => 'rsi', 'Rhsim11G0036600' => 'rsi', 'Rhsim12G0014900' => 'rsi', 'RhsimUnG0006500' => 'rsi', 'RhsimUnG0090400' => 'rsi', 'RhsimUnG0116400' => 'rsi', 'Sabra01G0180800' => 'sbr', 'Sabra06G0005000' => 'sbr', 'Sabra06G0094300' => 'sbr', 'Sabra13G0069700' => 'sbr', 'SalBow1G1247' => 'sbo', 'SalBow3G1680' => 'sbo', 'SalBow4G1488' => 'sbo', 'SalBow7G2432' => 'sbo', 'SalBow7G4792' => 'sbo', 'Sc03g0005510' => 'sci', 'Sc09g0001630' => 'sci', 'Sc09g0001650' => 'sci', 'Sc20g0005820' => 'sci', 'Sc21g0000770' => 'sci', 'Sed0008250' => 'sed', 'Sed0014925' => 'sed', 'Sed0015103' => 'sed', 'Sed0016129' => 'sed', 'Sed0016380' => 'sed', 'Sed0023390' => 'sed', 'SEGI_02747' => 'sgi', 'SEGI_12277' => 'sgi', 'SEGI_13377' => 'sgi', 'SEGI_25701' => 'sgi', 'SEGI_32977' => 'sgi', 'SGA_v2.0_scaffold13G06352' => 'sas', 'SGA_v2.0_scaffold73G24426' => 'sas', 'SGA_v2.0_scaffold96G29093' => 'sas', 'SMO119G0427' => 'smo', 'SMO276G0038' => 'smo', 'SMO339G0033' => 'smo', 'SMO351G0009' => 'smo', 'Solyc04g051190.3' => 'sly', 'Solyc05g016330.3' => 'sly', 'Solyc08g075440.4' => 'sly', 'Solyc10g083790.3' => 'sly', 'Solyc11g040223.1' => 'sly', 'Sopen04g022560' => 'spe', 'Sopen05g013440' => 'spe', 'Sopen05g013460' => 'spe', 'Sopen08g024070' => 'spe', 'Sopen10g033240' => 'spe', 'Sopen11g017990' => 'spe', 'Sopen11g018010' => 'spe', 'Sp1g27470' => 'spa', 'Sp1g27490' => 'spa', 'Sp2g01830' => 'spa', 'Sp5g09190' => 'spa', 'Sp7g13340' => 'spa', 'TAR362G0187' => 'tar', 'TAR365G0232' => 'tar', 'TAR375G1104' => 'tar', 'TAR623G0464' => 'tar', 'TAR626G0594' => 'tar', 'THA.LOC104798522' => 'tha', 'THA.LOC104808510' => 'tha', 'THA.LOC104814399' => 'tha', 'THA.LOC104818583' => 'tha', 'Thecc.01G173300' => 'tca', 'Thecc.03G318700' => 'tca', 'Thecc.05G074700' => 'tca', 'Thecc.05G203300' => 'tca', 'Thhalv10006980m.g' => 'esa', 'Thhalv10007138m.g' => 'esa', 'Thhalv10010267m.g' => 'esa', 'Thhalv10023482m.g' => 'esa', 'Thhalv10024764m.g' => 'esa', 'TPR.G11479' => 'tpr', 'TPR.G22456' => 'tpr', 'TPR.G29411' => 'tpr', 'TPR.G38037' => 'tpr', 'TPR.G8989' => 'tpr', 'TWI14G0457' => 'twi', 'TWI32G0878' => 'twi', 'TWI59G0800' => 'twi', 'TWI74G0518' => 'twi', 'TWI79G0428' => 'twi', 'unitig_22.g5107' => 'ugi', 'unitig_748.g7392' => 'ugi', 'unitig_899.g15286' => 'ugi', 'vmacro00085' => 'vma', 'vmacro08759' => 'vma', 'vmacro08803' => 'vma', 'vmacro19610' => 'vma', 'VMungo0720G0039' => 'vmu', 'VMungo1215G1610' => 'vmu', 'VMungo1215G2273' => 'vmu', 'VMungo1383G3642' => 'vmu', 'Zm00001eb009310' => 'zma', 'Zm00001eb207080' => 'zma', 'Zm00001eb258960' => 'zma', 'Zm00001eb399610' => 'zma' ) $gf_id = 'HOM05D001176' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001176' ) $data_identifier = 'HOM05D001176' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 3, 'aag' => (int) 5, 'ach' => (int) 5, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 4, 'arhy' => (int) 8, 'ath' => (int) 4, 'atr' => (int) 9, 'acertr' => (int) 4, 'cqu' => (int) 9, 'bca' => (int) 14, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 7, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 6, 'cbr' => (int) 6, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 4, 'col' => (int) 5, 'cpa' => (int) 5, 'cre' => (int) 7, 'csa' => (int) 5, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 10, 'ghi' => (int) 9, 'gra' => (int) 4, 'vvi' => (int) 4, 'han' => (int) 4, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 5, 'lonja' => (int) 4, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 4, 'mpo' => (int) 4, 'mbi' => (int) 7, 'mco' => (int) 6, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 4, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 8, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 4, 'pco' => (int) 6, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 10, 'sbr' => (int) 4, 'sbo' => (int) 5, 'sci' => (int) 5, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 3, 'smo' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 7, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb399610' $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